An anisotropic nanopatterning method, based on a technique of atomic force microscopy (AFM) scribing of a thin polyimide film, is used to generate an alignment layer whose topography depends on the writing direction. Detailed experimental measurements are presented for the topographical anisotropy that arises when the polyimide alignment layer is scribed parallel and antiparallel to the AFM cantilever orientation. By means of a novel nanotomographic approach, the optical retardation δ of an alignable birefringent liquid that covers the scribed substrate is measured with unprecedented resolution of only a few tens of nanometers. In this technique a thin optical fiber is raster-scanned at several fixed heights inside the birefringent liquid, and the transmitted polarized light is collected downstream. The optical retardation δ from the fiber's tip to the polyimide interface was measured as a function of position x,y,z, with the results reflecting the spatially varying depth of the medium due to the polymer film surface topography. Theoretical calculations for δ are in excellent agreement with both the topographical and the high resolution nanoimaging experimental results obtained.